| 1 |
function [S] = rdmnc(varargin) |
| 2 |
|
| 3 |
% Usage: |
| 4 |
% S=RDMNC(FILE1,FILE2,...) |
| 5 |
% S=RDMNC(FILE1,...,ITER) |
| 6 |
% S=RDMNC(FILE1,...,'VAR1','VAR2',...) |
| 7 |
% S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER) |
| 8 |
% |
| 9 |
% Input: |
| 10 |
% FILE1 Either a single file name (e.g. 'state.nc') or a wild-card |
| 11 |
% strings expanding to a group of file names (e.g. 'state.*.nc'). |
| 12 |
% There are no assumptions about suffices (e.g. 'state.*' works). |
| 13 |
% VAR1 Model variable names as written in the MNC/netcdf file. |
| 14 |
% ITER Vector of iterations in the MNC/netcdf files, not model time. |
| 15 |
% |
| 16 |
% Output: |
| 17 |
% S Structure with fields corresponding to 'VAR1', 'VAR2', ... |
| 18 |
% |
| 19 |
% Description: |
| 20 |
% This function is a rudimentary wrapper for joining and reading netcdf |
| 21 |
% files produced by MITgcm. It does not give the same flexibility as |
| 22 |
% opening the netcdf files directly using netcdf(), but is useful for |
| 23 |
% quick loading of entire model fields which are distributed in multiple |
| 24 |
% netcdf files. |
| 25 |
% |
| 26 |
% Example: |
| 27 |
% >> S=rdmnd('state.*','XC','YC','T'); |
| 28 |
% >> imagesc( S.XC, S.YC, S.T(:,:,1)' ); |
| 29 |
% |
| 30 |
% Author: Alistair Adcroft |
| 31 |
% Modifications: Daniel Enderton |
| 32 |
|
| 33 |
% $Header: /u/gcmpack/MITgcm/utils/matlab/rdmnc.m,v 1.19 2009/11/24 13:09:16 mlosch Exp $ |
| 34 |
% $Name: $ |
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|
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% Initializations |
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dBug=0; |
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file={}; |
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filepaths={}; |
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files={}; |
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varlist={}; |
| 42 |
iters=[]; |
| 43 |
|
| 44 |
% find out if matlab's generic netcdf API is available |
| 45 |
% if not assume that Chuck Denham's netcdf toolbox is installed |
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usemexcdf = isempty(which('netcdf.open')); |
| 47 |
|
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% Process function arguments |
| 49 |
for iarg=1:nargin; |
| 50 |
arg=varargin{iarg}; |
| 51 |
if ischar(arg) |
| 52 |
if isempty(dir(char(arg))) |
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varlist{end+1}=arg; |
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else |
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file{end+1}=arg; |
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end |
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else |
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if isempty(iters) |
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iters=arg; |
| 60 |
else |
| 61 |
error(['The only allowed numeric argument is iterations',... |
| 62 |
' to read in as a vector for the last argument']); |
| 63 |
end |
| 64 |
end |
| 65 |
end |
| 66 |
if isempty(file) |
| 67 |
if isempty(varlist), |
| 68 |
fprintf( 'No file name in argument list\n'); |
| 69 |
else |
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fprintf(['No file in argument list:\n ==> ',char(varlist(1))]); |
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for i=2:size(varlist,2), fprintf([' , ',char(varlist(i))]); end |
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fprintf(' <==\n'); |
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end |
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error(' check argument list !!!'); |
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end |
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|
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% Create list of filenames |
| 78 |
for eachfile=file |
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filepathtemp=eachfile{:}; |
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indecies = find(filepathtemp==filesep); |
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if ~isempty(indecies) |
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filepathtemp = filepathtemp(1:indecies(end)); |
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else |
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filepathtemp = ''; |
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end |
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expandedEachFile=dir(char(eachfile{1})); |
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for i=1:size(expandedEachFile,1); |
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if expandedEachFile(i).isdir==0 |
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files{end+1}=expandedEachFile(i).name; |
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filepaths{end+1}=filepathtemp; |
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end |
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end |
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end |
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|
| 95 |
|
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% If iterations unspecified, open all the files and make list of all the |
| 97 |
% iterations that appear, use this iterations list for data extraction. |
| 98 |
if isempty(iters) |
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iters = []; |
| 100 |
for ieachfile=1:length(files) |
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eachfile = [filepaths{ieachfile},files{ieachfile}]; |
| 102 |
if usemexcdf |
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nc=netcdf(char(eachfile),'read'); |
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nciters = nc{'iter'}(:); |
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if isempty(nciters), nciters = nc{'T'}(:); end |
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else |
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nc=netcdf.open(char(eachfile),'NC_NOWRITE'); |
| 108 |
nciters = ncgetvar(nc,'iter'); |
| 109 |
if isempty(nciters), nciters = ncgetvar(nc,'T'); end |
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end |
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iters = [iters,nciters']; |
| 112 |
if usemexcdf |
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close(nc); |
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else |
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netcdf.close(nc); |
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end |
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end |
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iters = unique(iters'); |
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end |
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|
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% Cycle through files for data extraction. |
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S.attributes=[]; |
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for ieachfile=1:length(files) |
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eachfile = [filepaths{ieachfile},files{ieachfile}]; |
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if dBug > 0, fprintf([' open: ',eachfile]); end |
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if usemexcdf |
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nc=netcdf(char(eachfile),'read'); |
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S=rdmnc_local(nc,varlist,iters,S,dBug); |
| 129 |
close(nc); |
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else |
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nc=netcdf.open(char(eachfile),'NC_NOWRITE'); |
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S=rdmnc_local_matlabAPI(char(eachfile),nc,varlist,iters,S,dBug); |
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netcdf.close(nc); |
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end |
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end |
| 136 |
|
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return |
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|
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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% Local functions % |
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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|
| 143 |
function [A] = read_att(nc); |
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allatt=ncnames(att(nc)); |
| 145 |
if ~isempty(allatt) |
| 146 |
for attr=allatt; |
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A.(char(attr))=nc.(char(attr))(:); |
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end |
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else |
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A = 'none'; |
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end |
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|
| 153 |
function [i0,j0,fn] = findTileOffset(S); |
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fn=0; |
| 155 |
if isfield(S,'attributes') & isfield(S.attributes,'global') |
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G=S.attributes.global; |
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tn=G.tile_number; |
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snx=G.sNx; sny=G.sNy; nsx=G.nSx; nsy=G.nSy; npx=G.nPx; npy=G.nPy; |
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ntx=nsx*npx;nty=nsy*npy; |
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gbi=mod(tn-1,ntx); gbj=(tn-gbi-1)/ntx; |
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i0=snx*gbi; j0=sny*gbj; |
| 162 |
if isfield(S.attributes.global,'exch2_myFace') |
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fn=G.exch2_myFace; |
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end |
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else |
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i0=0;j0=0; |
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end |
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%[snx,sny,nsx,nsy,npx,npy,ntx,nty,i0,j0,fn]; |
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|
| 170 |
function [S] = rdmnc_local(nc,varlist,iters,S,dBug) |
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|
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fiter = nc{'iter'}(:); % File iterations present |
| 173 |
if isempty(fiter), fiter = nc{'T'}(:); end |
| 174 |
if isinf(iters); iters = fiter(end); end |
| 175 |
if isnan(iters); iters = fiter; end |
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[fii,dii] = ismember(fiter,iters); fii = find(fii); % File iteration index |
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dii = dii(find(dii ~= 0)); % Data interation index |
| 178 |
if dBug > 0, |
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fprintf(' ; fii='); fprintf(' %i',fii); |
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fprintf(' ; dii='); fprintf(' %i',dii); fprintf(' \n'); |
| 181 |
end |
| 182 |
|
| 183 |
% No variables specified? Default to all |
| 184 |
if isempty(varlist), varlist=ncnames(var(nc)); end |
| 185 |
|
| 186 |
% Attributes for structure |
| 187 |
if iters>0; S.iters_from_file=iters; end |
| 188 |
S.attributes.global=read_att(nc); |
| 189 |
[pstr,netcdf_fname,ext] = fileparts(name(nc)); |
| 190 |
if strcmp(netcdf_fname(end-3:end),'glob') |
| 191 |
% assume it is a global file produced by gluemnc and change some |
| 192 |
% attributes |
| 193 |
S.attributes.global.sNx = S.attributes.global.Nx; |
| 194 |
S.attributes.global.sNy = S.attributes.global.Ny; |
| 195 |
S.attributes.global.nPx = 1; |
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S.attributes.global.nSx = 1; |
| 197 |
S.attributes.global.nPy = 1; |
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S.attributes.global.nSy = 1; |
| 199 |
S.attributes.global.tile_number = 1; |
| 200 |
S.attributes.global.nco_openmp_thread_number = 1; |
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end |
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|
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% Read variable data |
| 204 |
for ivar=1:size(varlist,2) |
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|
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cvar=char(varlist{ivar}); |
| 207 |
if isempty(nc{cvar}) |
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disp(['No such variable ''',cvar,''' in MNC file ',name(nc)]); |
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continue |
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end |
| 211 |
|
| 212 |
dims = ncnames(dim(nc{cvar})); % Dimensions |
| 213 |
sizVar = size(nc{cvar}); nDims=length(sizVar); |
| 214 |
if dims{1} == 'T' |
| 215 |
if isempty(find(fii)), error('Iters not found'); end |
| 216 |
it = length(dims); |
| 217 |
tmpdata = nc{cvar}(fii,:); |
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% leading unity dimensions get lost; add them back: |
| 219 |
tmpdata=reshape(tmpdata,[length(fii) sizVar(2:end)]); |
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else |
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it = 0; |
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tmpdata = nc{cvar}(:); |
| 223 |
% leading unity dimensions get lost; add them back: |
| 224 |
tmpdata=reshape(tmpdata,sizVar); |
| 225 |
end |
| 226 |
|
| 227 |
if dBug > 1, |
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fprintf([' var:',cvar,': nDims=%i ('],nDims);fprintf(' %i',size(nc{cvar})); |
| 229 |
fprintf('):%i,nD=%i,it=%i ;',length(size(tmpdata)),length(dims),it); |
| 230 |
end |
| 231 |
if length(dims) > 1, |
| 232 |
tmpdata=permute(tmpdata,[nDims:-1:1]); |
| 233 |
end |
| 234 |
if dBug > 1, |
| 235 |
% fprintf('(tmpdata:');fprintf(' %i',size(tmpdata)); fprintf(')'); |
| 236 |
end |
| 237 |
[ni nj nk nm nn no np]=size(tmpdata); |
| 238 |
|
| 239 |
[i0,j0,fn]=findTileOffset(S); |
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cdim=dims{end}; if cdim(1)~='X'; i0=0; end |
| 241 |
cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end |
| 242 |
if length(dims)>1; |
| 243 |
cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end |
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else |
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j0=0; |
| 246 |
end |
| 247 |
if dBug > 1, |
| 248 |
fprintf(' i0,ni= %i %i; j,nj= %i %i; nk=%i :',i0,ni,j0,nj,nk); |
| 249 |
end |
| 250 |
|
| 251 |
Sstr = ''; |
| 252 |
for istr = 1:max(nDims,length(dims)), |
| 253 |
if istr == it, Sstr = [Sstr,'dii,']; |
| 254 |
elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),']; |
| 255 |
elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),']; |
| 256 |
elseif istr == 3, Sstr = [Sstr,'(1:nk),']; |
| 257 |
elseif istr == 4, Sstr = [Sstr,'(1:nm),']; |
| 258 |
elseif istr == 5, Sstr = [Sstr,'(1:nn),']; |
| 259 |
elseif istr == 6, Sstr = [Sstr,'(1:no),']; |
| 260 |
elseif istr == 7, Sstr = [Sstr,'(1:np),']; |
| 261 |
else, error('Can''t handle this many dimensions!'); |
| 262 |
end |
| 263 |
end |
| 264 |
eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;']) |
| 265 |
%S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata; |
| 266 |
if dBug > 1, fprintf(' %i',size(S.(cvar))); fprintf('\n'); end |
| 267 |
|
| 268 |
S.attributes.(cvar)=read_att(nc{cvar}); |
| 269 |
% replace missing or FillValues with NaN |
| 270 |
if isfield(S.attributes.(cvar),'missing_value'); |
| 271 |
misval = S.attributes.(cvar).missing_value; |
| 272 |
S.(cvar)(S.(cvar) == misval) = NaN; |
| 273 |
end |
| 274 |
if isfield(S.attributes.(cvar),'FillValue_'); |
| 275 |
misval = S.attributes.(cvar).FillValue_; |
| 276 |
S.(cvar)(S.(cvar) == misval) = NaN; |
| 277 |
end |
| 278 |
|
| 279 |
end % for ivar |
| 280 |
|
| 281 |
if isempty(S) |
| 282 |
error('Something didn''t work!!!'); |
| 283 |
end |
| 284 |
|
| 285 |
return |
| 286 |
|
| 287 |
function [S] = rdmnc_local_matlabAPI(fname,nc,varlist,iters,S,dBug) |
| 288 |
|
| 289 |
fiter = ncgetvar(nc,'iter'); % File iterations present |
| 290 |
if isempty(fiter), fiter = ncgetvar(nc,'T'); end |
| 291 |
if isinf(iters); iters = fiter(end); end |
| 292 |
if isnan(iters); iters = fiter; end |
| 293 |
[fii,dii] = ismember(fiter,iters); fii = find(fii); % File iteration index |
| 294 |
dii = dii(find(dii ~= 0)); % Data interation index |
| 295 |
if dBug > 0, |
| 296 |
fprintf(' ; fii='); fprintf(' %i',fii); |
| 297 |
fprintf(' ; dii='); fprintf(' %i',dii); fprintf(' \n'); |
| 298 |
end |
| 299 |
|
| 300 |
% get basic information about netcdf file |
| 301 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
| 302 |
|
| 303 |
% No variables specified? Default to all |
| 304 |
if isempty(varlist), |
| 305 |
for k=0:nvars-1 |
| 306 |
varlist{k+1} = netcdf.inqVar(nc,k); |
| 307 |
end |
| 308 |
end |
| 309 |
|
| 310 |
% Attributes for structure |
| 311 |
if iters>0; S.iters_from_file=iters; end |
| 312 |
S.attributes.global=ncgetatt(nc,'global'); |
| 313 |
[pstr,netcdf_fname,ext] = fileparts(fname); |
| 314 |
if strcmp(netcdf_fname(end-3:end),'glob') |
| 315 |
% assume it is a global file produced by gluemnc and change some |
| 316 |
% attributes |
| 317 |
S.attributes.global.sNx = S.attributes.global.Nx; |
| 318 |
S.attributes.global.sNy = S.attributes.global.Ny; |
| 319 |
S.attributes.global.nPx = 1; |
| 320 |
S.attributes.global.nSx = 1; |
| 321 |
S.attributes.global.nPy = 1; |
| 322 |
S.attributes.global.nSy = 1; |
| 323 |
S.attributes.global.tile_number = 1; |
| 324 |
S.attributes.global.nco_openmp_thread_number = 1; |
| 325 |
end |
| 326 |
|
| 327 |
% Read variable data |
| 328 |
for ivar=1:size(varlist,2) |
| 329 |
|
| 330 |
cvar=char(varlist{ivar}); |
| 331 |
varid=ncfindvarid(nc,cvar); |
| 332 |
if isempty(varid) |
| 333 |
disp(['No such variable ''',cvar,''' in MNC file ',fname]); |
| 334 |
continue |
| 335 |
end |
| 336 |
|
| 337 |
[varname,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
| 338 |
|
| 339 |
% Dimensions |
| 340 |
clear sizVar dims |
| 341 |
for k=1:length(dimids) |
| 342 |
[dims{k}, sizVar(k)] = netcdf.inqDim(nc,dimids(k)); |
| 343 |
end |
| 344 |
if length(sizVar)==1; sizVar(2) = 1; end; |
| 345 |
nDims=length(sizVar); |
| 346 |
if dims{1} == 'T' |
| 347 |
if isempty(find(fii)), error('Iters not found'); end |
| 348 |
it = length(dims); |
| 349 |
tmpdata = netcdf.getVar(nc,varid,'double'); |
| 350 |
tmpdata = tmpdata(fii,:); |
| 351 |
% leading unity dimensions get lost; add them back: |
| 352 |
tmpdata=reshape(tmpdata,[length(fii) sizVar(2:end)]); |
| 353 |
else |
| 354 |
it = 0; |
| 355 |
tmpdata = netcdf.getVar(nc,varid,'double'); |
| 356 |
% leading unity dimensions get lost; add them back: |
| 357 |
tmpdata=reshape(tmpdata,sizVar); |
| 358 |
end |
| 359 |
|
| 360 |
if dBug > 1, |
| 361 |
fprintf([' var:',cvar,': nDims=%i ('],nDims);fprintf(' %i',sizVar); |
| 362 |
fprintf('):%i,nD=%i,it=%i ;',length(size(tmpdata)),length(dims),it); |
| 363 |
end |
| 364 |
[ni nj nk nm nn no np]=size(tmpdata); |
| 365 |
|
| 366 |
[i0,j0,fn]=findTileOffset(S); |
| 367 |
cdim=dims{1}; if cdim(1)~='X'; i0=0; end |
| 368 |
cdim=dims{1}; if cdim(1)=='Y'; i0=j0; j0=0; end |
| 369 |
if length(dims)>1; |
| 370 |
cdim=dims{2}; if cdim(1)~='Y'; j0=0; end |
| 371 |
else |
| 372 |
j0=0; |
| 373 |
end |
| 374 |
if dBug > 1, |
| 375 |
fprintf(' i0,ni= %i %i; j,nj= %i %i; nk=%i :',i0,ni,j0,nj,nk); |
| 376 |
end |
| 377 |
|
| 378 |
Sstr = ''; |
| 379 |
for istr = 1:max(nDims,length(dims)), |
| 380 |
if istr == it, Sstr = [Sstr,'dii,']; |
| 381 |
elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),']; |
| 382 |
elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),']; |
| 383 |
elseif istr == 3, Sstr = [Sstr,'(1:nk),']; |
| 384 |
elseif istr == 4, Sstr = [Sstr,'(1:nm),']; |
| 385 |
elseif istr == 5, Sstr = [Sstr,'(1:nn),']; |
| 386 |
elseif istr == 6, Sstr = [Sstr,'(1:no),']; |
| 387 |
elseif istr == 7, Sstr = [Sstr,'(1:np),']; |
| 388 |
else, error('Can''t handle this many dimensions!'); |
| 389 |
end |
| 390 |
end |
| 391 |
eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;']) |
| 392 |
%S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata; |
| 393 |
if dBug > 1, fprintf(' %i',size(S.(cvar))); fprintf('\n'); end |
| 394 |
|
| 395 |
S.attributes.(cvar)=ncgetatt(nc,cvar); |
| 396 |
% replace missing or FillValues with NaN |
| 397 |
if isfield(S.attributes.(cvar),'missing_value'); |
| 398 |
misval = S.attributes.(cvar).missing_value; |
| 399 |
S.(cvar)(S.(cvar) == misval) = NaN; |
| 400 |
end |
| 401 |
if isfield(S.attributes.(cvar),'FillValue_'); |
| 402 |
misval = S.attributes.(cvar).FillValue_; |
| 403 |
S.(cvar)(S.(cvar) == misval) = NaN; |
| 404 |
end |
| 405 |
|
| 406 |
end % for ivar |
| 407 |
|
| 408 |
if isempty(S) |
| 409 |
error('Something didn''t work!!!'); |
| 410 |
end |
| 411 |
|
| 412 |
return |
| 413 |
|
| 414 |
function vf = ncgetvar(nc,varname) |
| 415 |
% read a netcdf variable |
| 416 |
|
| 417 |
% find out basics about the files |
| 418 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
| 419 |
vf = []; |
| 420 |
varid = []; |
| 421 |
for k=0:nvars-1 |
| 422 |
if strcmp(netcdf.inqVar(nc,k),varname) |
| 423 |
varid = netcdf.inqVarId(nc,varname); |
| 424 |
end |
| 425 |
end |
| 426 |
if ~isempty(varid); |
| 427 |
[varn,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
| 428 |
% get data |
| 429 |
vf = double(netcdf.getVar(nc,varid)); |
| 430 |
else |
| 431 |
% do nothing |
| 432 |
end |
| 433 |
|
| 434 |
return |
| 435 |
|
| 436 |
function misval = ncgetmisval(nc,varid) |
| 437 |
|
| 438 |
[varname,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
| 439 |
misval = []; |
| 440 |
for k=0:natts-1 |
| 441 |
attn = netcdf.inqAttName(nc,varid,k); |
| 442 |
if strcmp(attn,'missing_value') | strcmp(attn,'_FillValue') |
| 443 |
misval = double(netcdf.getAtt(nc,varid,attname)); |
| 444 |
end |
| 445 |
end |
| 446 |
|
| 447 |
function A = ncgetatt(nc,varname) |
| 448 |
% get all attributes and put them into a struct |
| 449 |
|
| 450 |
% 1. get global properties of file |
| 451 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
| 452 |
|
| 453 |
% get variable ID and properties |
| 454 |
if strcmp('global',varname) |
| 455 |
% "variable" is global |
| 456 |
varid = netcdf.getConstant('NC_GLOBAL'); |
| 457 |
else |
| 458 |
% find variable ID and properties |
| 459 |
varid = ncfindvarid(nc,varname); |
| 460 |
if ~isempty(varid) |
| 461 |
[varn,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
| 462 |
else |
| 463 |
warning(sprintf('variable %s not found',varname)) |
| 464 |
end |
| 465 |
end |
| 466 |
|
| 467 |
if natts > 1 |
| 468 |
for k=0:natts-1 |
| 469 |
attn = netcdf.inqAttName(nc,varid,k); |
| 470 |
[xtype attlen]=netcdf.inqAtt(nc,varid,attn); |
| 471 |
attval = netcdf.getAtt(nc,varid,attn); |
| 472 |
if ~ischar(attval) |
| 473 |
attval = double(attval); |
| 474 |
end |
| 475 |
A.(char(attn))=attval; |
| 476 |
end |
| 477 |
else |
| 478 |
A = 'none'; |
| 479 |
end |
| 480 |
|
| 481 |
return |
| 482 |
|
| 483 |
|
| 484 |
function varid = ncfindvarid(nc,varname) |
| 485 |
|
| 486 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
| 487 |
varid=[]; |
| 488 |
for k=0:nvars-1 |
| 489 |
if strcmp(netcdf.inqVar(nc,k),varname); |
| 490 |
varid = netcdf.inqVarId(nc,varname); |
| 491 |
break |
| 492 |
end |
| 493 |
end |
| 494 |
|
| 495 |
return |
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